Enemy Mine has been considered a possible influence behind Star Trek Beyond. The Enterprise crew are stranded on an alien planet when they are attacked by hostile aliens from that world.

In the previous two movies, there were only subtle references to the prequel series [Star Trek: Enterprise], which takes place 112 years prior to Star Trek Beyond. Captain Jonathan Archer was mentioned in Star Trek, and a model of his ship was seen in Star Trek Into Darkness. However, Star Trek Beyond features quite a few substantial connections.* Scotty mentions M.A.C.O. (Military Assault Command Operations), which was a military unit in the last two seasons of the series.* Krall was a member of the M.A.C.O.s back when he was still Balthazar Edison, before being given the USS Franklin.* Krall mentions the Xindi and Romulan Wars when fighting against James T. Kirk at Yorktown; the Xindi storyline was featured in the third season of the series, raising the possibility that Edison was one of the M.A.C.O.s on board the Enterprise NX-01, the namesake starship from the series.* The Romulan Wars were supposed to be featured in the series' fifth season, before this got canceled.* The design and size of the USS Franklin is very close to the Enterprise NX-01, and the uniforms that its crew can be seen wearing on the video look much closer to the blue jumpsuits featured on Star Trek: Enterprise.* Scotty mentions that the transporters on the Franklin were only used for cargo; indeed, the Enterprise NX-01 was the first ship with a transporter system that was cleared for use by living beings, so older ships would not have had those.* Like the Enterprise NX-01, the USS Franklin has polarized hull plating instead of deflector shields, as well as phase cannons and conventional torpedoes instead of phasers and photon torpedoes.* Lastly, the USS Franklin is mentioned to be a Warp 4 vessel; by the time that Edison became captain of her, the ship must have been older than 10 years, and most starships were at least Warp 5 or higher by then. Being offered an obsolete cargo ship could have added to Edison's feeling of abandonment by the Federation.

Despite being the third movie of the rebooted franchise, this movie marks the second time the Enterprise has been destroyed, rebuilt and christened "NCC-1701-A". The first was Star Trek III: The Search for Spock where the original 1701 was destroyed and rebuilt with "1701-A" which made its appearance in Star Trek IV: The Voyage Home.

In this film, Sulu (John Cho) is revealed to have a daughter. In Star Trek: Generations, Sulu (George Takei) is also revealed to have a daughter (she operates the helm on the Enterprise-B).

Writer Simon Pegg and director Justin Lin made the decision of making Sulu gay as a nod to original actor George Takei, who has since become a prominent LGBT rights activist. However, Takei has since stated his disagreement with this decision as that was not Gene Roddenberry's intention for the character Hikaru Sulu.

The limited edition poster which features Kirk, Spock and Jaylah is a homage to the original poster for Star Trek: The Motion Picture with Kirk, Spock and Ilia.

A reference is made to the episode [Star Trek]: {The Trouble with Tribbles}: When McCoy remarks to Kirk that he "took this from Chekov's locker" (referring to the bottle of alcohol), Kirk responds to the effect "I would have pegged Chekov as a vodka man..." as both are surprised by the type of alcohol that Chekov drinks. This is confirmed as scotch in the final party scene when Chekov remarks that "It was invented by a little old lady in Russia". In the original episode, Chekov and Scotty sit in the Space Station K-7 bar as Scotty states that Chekov "get off that milk diet" and have scotch instead since it was "a drink for a man". Chekov replies that "it was invented by a little old lady from Leningrad".

According to Idris Elba in a Facebook live chat with Zoe Saldana, the black eye that Chris Pine has in the final fight scene with Idris Elba is not makeup, it's a real black eye that Pine got when they got a little too rough during filming.

Alice Eve does not return as Dr. Carol Marcus. During this film, she is not mentioned and her absence is unexplained. In the ending of the previous film Star Trek Into Darkness, Carol became a member of the Enterprise crew and joined them on their five-year mission.

The reference about the USS Franklin coming to be on the planet by "some green space hand" is a reference to the episode [Star Trek]: {Who Mourns for Adonais?}.

Simon Pegg identified the space station as "Starbase Yorktown" in early interviews. "Yorktown" was the original name of the starship in Gene Roddenberry's early script treatments for the original [Star Trek] series, before this was changed to "Enterprise".

When Kirk and crew first enter Yorktown's reception area, an announcement can be heard over the intercom referring to a starship with registry number NCC-2893 just arriving. This is a reference to the USS Stargazer (NCC-2893), the first ship that Captain Jean-Luc Picard commanded on [Star Trek: The Next Generation]. While the USS Franklin's registry number NX-326 pays homage to Leonard Nimoy as his birthday is March 26 or 3-26.

In an interview, Karl Urban stated that he almost did not return to the role of Dr. Leonard "Bones" McCoy. What convinced him to stay was a discussion with director Justin Lin.

According to Zachary Quinto, while he greatly enjoys the character Spock, he has made mention that he is ready to move on from the role and venture into other projects. He has stated though that he fully plans to finish out his contractual obligations in playing the role of Spock and seeing where his character's journey goes in the trilogy. Quinto (just like the rest of his main co-stars) signed on for a three picture deal, which makes this film his last contractual commitment towards the role of Spock. However, he has since signed on for a fourth movie.

Simon Pegg revealed in a press conference that the character Jaylah, was inspired by Jennifer Lawrence in the film Winter's Bone. "We were trying to create this very independent character. But we didn't have a name for it," Pegg said. "So we just called it 'Jennifer-Lawrence-In-Winter's-Bone.'" "That's a long name," the writer and actor joked. "So it started getting tiring always saying, well Jennifer-Lawrence-In-Winter's-Bone is fighting here. So then we started calling her J-Law. And then she became Jaylah."

On June 19, 2016, after production on the film was completed and a month before the film's release, Anton Yelchin died in a freak car accident. During the ending credits, there is a dedication caption which reads, "For Anton." The toast Kirk makes to absent friends at the very end is immediately followed by a shot on Anton Yelchin.